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Questions - bioinformatics

how to convert imputed dosage files to plink format files

I am trying to convert imputed dosage file from michigan imputation server to plink files. For this purpuse I am using a tool called dosageconvertor. I tried to install it using the commands: > git...
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Rhea Bedi

linux

installation

bioinformatics

genetics

vcf-variant-call-format

Votes: 0

Answers: 0

Where should you put you cache for ensembl-vep using conda

I've installed vep in conda like so: conda install ensembl-vep=105.0-0 And then I installed the human cache like so: vep_install -a cf -s homo_sapiens -y GRCh38 -c /mnt/gpfs/live/rd01__/ritd-ag-proje...
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Mike

conda

bioinformatics

vep

Votes: 0

Answers: 1

Latest Answer

I've got this working. The cache went into the vet home directory like so: vep_install -a cf -s homo_sapiens -y GRCh38 -c /mnt/gpfs/live/rd01__/ritd-ag-project-rd018o-mdflo13/refs/vep —CONVERT And th...
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Mike

Cannot import name 'TextFace' error while using ETE3 for Phylogeny Tree

I am trying to install ETE3 for phylogeny analysis but while installing it is showing error:cannot import name 'TextFace' I tried all the available options but could not succeed. Any help will be appr...
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shivam

python

bioinformatics

fasta

phylogeny

ete3

Votes: 0

Answers: 0

Count the number of times a substring appears in a file and place it in a new column

Question: I have 2 files, file 1 is a TSV (BED) file that has 23 base-pair sequences in column 7, for example: 1 779692 779715 Sample_3 + 1 ATGGTGCTTTGTTATGGCAGCTC 1 783462 783485 Sample_4 - 1 ATGA...
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KLM117

string

awk

grep

substring

bioinformatics

Votes: 0

Answers: 3

Latest Answer

I'd reach for a programming language like Perl. #!/usr/bin/perl use warnings; use strict; my ($fasta_file, $bed_file) = @ARGV; open my $fasta, '<', $fasta_file or die "$fasta_file: $!"; ...
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choroba

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